CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations.

IF 2.7 4区医学 Q2 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Neuroinformatics Pub Date : 2023-07-01 DOI:10.1007/s12021-023-09627-5

Laura Keto, Tiina Manninen

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Abstract

Understanding functions of astrocytes can be greatly enhanced by building and simulating computational models that capture their morphological details. Novel computational tools enable utilization of existing morphological data of astrocytes and building models that have appropriate level of details for specific simulation purposes. In addition to analyzing existing computational tools for constructing, transforming, and assessing astrocyte morphologies, we present here the CellRemorph toolkit implemented as an add-on for Blender, a 3D modeling platform increasingly recognized for its utility for manipulating 3D biological data. To our knowledge, CellRemorph is the first toolkit for transforming astrocyte morphologies from polygonal surface meshes into adjustable surface point clouds and vice versa, precisely selecting nanoprocesses, and slicing morphologies into segments with equal surface areas or volumes. CellRemorph is an open-source toolkit under the GNU General Public License and easily accessible via an intuitive graphical user interface. CellRemorph will be a valuable addition to other Blender add-ons, providing novel functionality that facilitates the creation of realistic astrocyte morphologies for different types of morphologically detailed simulations elucidating the role of astrocytes both in health and disease.

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cell䲟:一个工具箱转换，选择，切片三维细胞结构的道路上形态详细星形胶质细胞模拟。

通过建立和模拟能够捕捉星形胶质细胞形态细节的计算模型，可以大大增强对星形胶质细胞功能的理解。新的计算工具能够利用星形胶质细胞的现有形态学数据和建立具有适当细节水平的模型，用于特定的模拟目的。除了分析现有的用于构建、转换和评估星形胶质细胞形态的计算工具外，我们在这里提出了cell䲟工具包，作为Blender的附加组件，这是一个3D建模平台，因其在操纵3D生物数据方面的效用而日益得到认可。据我们所知，cell䲟是第一个将星形胶质细胞形态从多边形表面网格转换为可调表面点云的工具包，反之亦然，精确选择纳米工艺，并将形态切片成具有相同表面积或体积的片段。cellmurph是一个基于GNU通用公共许可证的开源工具包，可以通过直观的图形用户界面轻松访问。cell懊悔将是一个有价值的附加到其他搅拌机附加组件，提供新颖的功能，促进创建现实的星形胶质细胞形态不同类型的形态详细模拟阐明星形胶质细胞在健康和疾病中的作用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Neuroinformatics 医学-计算机：跨学科应用

CiteScore

6.00

自引率

6.70%

发文量

审稿时长

3 months

期刊介绍： Neuroinformatics publishes original articles and reviews with an emphasis on data structure and software tools related to analysis, modeling, integration, and sharing in all areas of neuroscience research. The editors particularly invite contributions on: (1) Theory and methodology, including discussions on ontologies, modeling approaches, database design, and meta-analyses; (2) Descriptions of developed databases and software tools, and of the methods for their distribution; (3) Relevant experimental results, such as reports accompanie by the release of massive data sets; (4) Computational simulations of models integrating and organizing complex data; and (5) Neuroengineering approaches, including hardware, robotics, and information theory studies.